Rename Layer to KmerLayer across obikindex and obikphylo

This commit renames the `Layer` type to `KmerLayer` throughout the `obikindex` and `obikphylo` crates. All imports, struct fields, function signatures, pattern matches, and instantiation calls have been updated accordingly. The change is a purely structural refactor that tightens type constraints without altering runtime behavior or data models.

src/obikindexer/src/algorithms/partitionner/router.rs

@@ -1,12 +1,12 @@
 use std::io;
 use std::path::PathBuf;
-use std::sync::atomic::{AtomicU32, AtomicU64, Ordering};
 use std::sync::Arc;
+use std::sync::atomic::{AtomicU32, AtomicU64, Ordering};
 use std::time::Instant;
 
 use obikindex::KmerIndex;
+use obikindex::layer::KmerLayer;
 use obikseq::RoutableSuperKmer;
-use obikindex::layer::Layer;
 use obiskio::SKResult;
 use obisys::Progress;
 use tracing::info;
@@ -15,7 +15,7 @@ use niffler::Level;
 use niffler::send::compression::Format;
 use obiskio::SKFileWriter;
 
-use obipipeline::{throttle, ThrottleGuard, Throttled};
+use obipipeline::{ThrottleGuard, Throttled, throttle};
 use obiread::NucPage;
 
 // ── Pipeline plumbing, private to `run` ─────────────────────────────────────
@@ -240,13 +240,19 @@ impl<'a> PartitionRouter<'a> {
                 let now = Instant::now();
                 if now.duration_since(last_report).as_secs_f64() > REPORT_INTERVAL {
                     last_report = now;
-                    cb(Progress { position: total_bases, total: None });
+                    cb(Progress {
+                        position: total_bases,
+                        total: None,
+                    });
                 }
             }
             self.write_batch(batch)?;
         }
         if let Some(cb) = on_progress.as_mut() {
-            cb(Progress { position: total_bases, total: None });
+            cb(Progress {
+                position: total_bases,
+                total: None,
+            });
         }
         self.close()
     }
@@ -272,7 +278,7 @@ impl<'a> PartitionRouter<'a> {
     fn ensure_writer(&mut self, partition: usize) -> SKResult<&mut SKFileWriter> {
         if self.writers[partition].is_none() {
             let dir = self.layer0_dir(partition);
-            Layer::create(&dir).map_err(|e| io::Error::other(e.to_string()))?;
+            KmerLayer::create(&dir).map_err(|e| io::Error::other(e.to_string()))?;
             let file_path = obikindex::layer::raw_superkmers_path(&dir);
             let writer = SKFileWriter::create_with(file_path, Format::Zstd, self.level)?;
             self.writers[partition] = Some(writer);